Mercurial > repos > bgruening > hicexplorer_hicadjustmatrix

comparison hicAdjustMatrix.xml @ 6:a7fd644deda6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:30:48 +0000
parents cc52e4ded146
children 2dccb6bb0add
comparison
equal deleted inserted replaced
5:794bd416f6c3 6:a7fd644deda6
1 <tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>adjust the shape of a Hi-C matrix</description> 2 <description>adjust the shape of a Hi-C matrix</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicAdjustMatrix</token> 4 <token name="@BINARY@">hicAdjustMatrix</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
20 --chromosomes '$chroms' 20 --chromosomes '$chroms'
21 #end if 21 #end if
22 #end if 22 #end if
23 23
24 #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile": 24 #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile":
25 --regions '$chromosomeOrRegionFile_conditional.regions' 25 --regions '$chromosomeOrRegionFile_conditional.regions'
26 #end if 26 #end if
27 27
28 && mv "$matrix_file_out" matrix 28 && mv '$matrix_file_out' matrix
29 ]]> 29 ]]>
30 </command> 30 </command>
31 <inputs> 31 <inputs>
32 <expand macro='matrix_h5_cooler_macro' /> 32 <expand macro='matrix_h5_cooler_macro' />
33 <param name="action_selector" type="select" label="Apply action" > 33 <param name="action_selector" type="select" label="Apply action">
34 <option value="keep" selected="True">keep</option> 34 <option value="keep" selected="True">keep</option>
35 <option value="remove">remove</option> 35 <option value="remove">remove</option>
36 <option value="mask">mask</option> 36 <option value="mask">mask</option>
37 </param> 37 </param>
38 <conditional name="chromosomeOrRegionFile_conditional"> 38 <conditional name="chromosomeOrRegionFile_conditional">
39 <param name="chromosomeOrRegionFile_selector" type="select" label="List of chromosomes or a BED file containg regions"> 39 <param name="chromosomeOrRegionFile_selector" type="select" label="List of chromosomes or a BED file containg regions">
40 <option value="optionChromosomes">Chromosomes</option> 40 <option value="optionChromosomes">Chromosomes</option>
41 <option value="optionRegionFile" selected="True">Region BED file</option> 41 <option value="optionRegionFile" selected="True">Region BED file</option>
42 </param> 42 </param>
43 <when value="optionChromosomes"> 43 <when value="optionChromosomes">
44 <repeat name="chromosomeOrder" min="0" title="Chromosomes to keep / remove / mask" 44 <repeat name="chromosomeOrder" min="0" title="Chromosomes to keep / remove / mask" help="The selected option will be applied on the selected chromosomes.">
45 help="The selected option will be applied on the selected chromosomes." > 45 <param name="chromosome" type="text">
46 <param name="chromosome" type="text" >
47 <validator type="empty_field" /> 46 <validator type="empty_field" />
48 </param> 47 </param>
49 </repeat> 48 </repeat>
50
51 </when> 49 </when>
52 <when value="optionRegionFile"> 50 <when value="optionRegionFile">
53 <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered." 51 <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered" help="Should contain the regions which should be kept, removed or masked." />
54 help="Should contain the regions which should be kept, removed or masked." />
55
56 </when> 52 </when>
57 </conditional> 53 </conditional>
58 </inputs> 54 </inputs>
59 <outputs> 55 <outputs>
60 <data name="outFileName" from_work_dir="matrix" format="h5"> 56 <data name="outFileName" from_work_dir="matrix" format="h5">
61 <change_format> 57 <change_format>
62 <when input="matrix_h5_cooler.ext" value="cool" format="cool" /> 58 <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
63 </change_format> 59 </change_format>
64 </data> 60 </data>
65 </outputs> 61 </outputs>
66 <tests> 62 <tests>
67 <test> 63 <test expect_num_outputs="1">
68 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> 64 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
69 <param name="action_selector" value="keep" /> 65 <param name="action_selector" value="keep" />
70 <conditional name="chromosomeOrRegionFile_conditional"> 66 <conditional name="chromosomeOrRegionFile_conditional">
71 <param name="chromosomeOrRegionFile_selector" value='optionChromosomes'/> 67 <param name="chromosomeOrRegionFile_selector" value='optionChromosomes' />
72 <repeat name="chromosomeOrder"> 68 <repeat name="chromosomeOrder">
73 <param name="chromosome" value='chrX'/> 69 <param name="chromosome" value='chrX' />
74 <param name="chromosome" value='chr3R'/> 70 <param name="chromosome" value='chr3R' />
75 </repeat> 71 </repeat>
76 </conditional> 72 </conditional>
77
78 <output name="outFileName" ftype="h5"> 73 <output name="outFileName" ftype="h5">
79 <assert_contents> 74 <assert_contents>
80 <has_h5_keys keys='intervals,matrix'/> 75 <has_h5_keys keys='intervals,matrix' />
81 </assert_contents> 76 </assert_contents>
82 </output> 77 </output>
83 </test> 78 </test>
84 79 <test expect_num_outputs="1">
85 <test> 80 <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
86 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
87 <param name="action_selector" value="mask" /> 81 <param name="action_selector" value="mask" />
88 <conditional name="chromosomeOrRegionFile_conditional"> 82 <conditional name="chromosomeOrRegionFile_conditional">
89 <param name="chromosomeOrRegionFile_selector" value='optionRegionFile'/> 83 <param name="chromosomeOrRegionFile_selector" value='optionRegionFile' />
90 <param name="regions" value='regions.bed'/> 84 <param name="regions" value='regions.bed' />
91 </conditional> 85 </conditional>
92
93 <output name="outFileName" ftype="h5"> 86 <output name="outFileName" ftype="h5">
94 <assert_contents> 87 <assert_contents>
95 <has_h5_keys keys='intervals,matrix,nan_bins'/> 88 <has_h5_keys keys='intervals,matrix,nan_bins' />
96 </assert_contents> 89 </assert_contents>
97 </output> 90 </output>
98 </test> 91 </test>
99 </tests> 92 </tests>
100 <help><![CDATA[ 93 <help><![CDATA[
107 _________________ 100 _________________
108 101
109 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 102 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
110 103
111 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 104 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
112 ]]></help> 105 ]]> </help>
113 <expand macro="citations" /> 106 <expand macro="citations" />
114 </tool> 107 </tool>